GgaINT1014994 @ galGal4
Intron Retention
Gene
ENSGALG00000026100 | HOXC11
Description
homeobox C11 [Source:HGNC Symbol;Acc:HGNC:5123]
Coordinates
AADN03020675.1:7777-12443:+
Coord C1 exon
AADN03020675.1:7777-8840
Coord A exon
AADN03020675.1:8841-10173
Coord C2 exon
AADN03020675.1:10174-12443
Length
1333 bp
Sequences
Splice sites
5' ss Seq
CGAGTAGGT
5' ss Score
5.76
3' ss Seq
TGCCTTCTGGTTCTTTTAAGGTG
3' ss Score
10.84
Exon sequences
Seq C1 exon
CCCGCTGAAAGCAGAAAGCAGAATCCGAATGGGAAGGAGAGGAGGAAGGAGGAAAAAAAAAAGAAAGGCAACTTCACGGCCGCCCCTCATAGTTGTGCTGTGAGCGCCTACGAGGGGTGTGCCTTCGGGAAAATGCATACAAATCTGCCATTGATTTTCATAATGTTTCTGCGGTGTTTGAAAACCAATCGTTTGAACCTCTGAGATCTTACCTAAGTGAACCACTCCTACGCATCTAAGTGCTCCAAACTGATATATGACAATATCTACTTTGGATCACGTGTTCCTCCGGAGCGACTAAGACGGATCGCGCGTCATCTCGCCTTCCCAAATTTTTTCCCCTCCGCACATCGGATCCAAAACATCTATCTATAGGAGCGAGAAAAGGAGAAAGATGTTTAACTCAGTGAATCTGGGCAACTTCTGCTCCCAGTCGCGTAAAGAGAGGAGCGCTGAGTTTGGAGAGCGGGCGGGTTGCGCTTCCAACCTCTACCTCCCCAGCTGTACCTATTACGTCCCCGAATTTTCAACTGTGTCATCTTTCCTGCCACAGGCCCCCTCTCGCCAAATCTCCTACCCGTACTCCACCAACCTCTCGCAGCCCGTGCGAGAGGTCTCCTATGGTCTAGACCCCTCCAGTAAATGGCACCATAGAAGCAATTACGCGTCGTGTTATTCCGCAGAAGATCTGATGCATAGAGAGTGCATCCCGCCTTCCACCATGACCGAAATGCTAATGAAAAACGAGAGCGCGTACAGCCACCACCACCCCAGCTCCAACCACCCGGCACCGACGGGATTCTACGGCGGCATGAACAAAAACACGGTCCTGCCCCAAGGCTTCGACCGCTTCTTCGAAAACGCGTATTGCGGGGCGGAAAACCCGACCGAGAGCTGCGGGCAGAAGGGAGAGGGCAAAGGGGAGGCTGAGCCCCAGAGCCACGCGCTGTCATCCCGCGGAGAGACGGGGATGGACCCGGAAGACGAAGAGGAGAACACAACTCCCGGCTCTTCAGCCTCGTCCTCCTCTGTCAACAAGGAAGGAAGCAAAAGCAGCAATTCGA
Seq A exon
GTAGGTAGAGCAGTAAACGGAAAGGTTAAGGGACTAGCCCGTGTGTTTTGTCGGTCAAATTTTATGTGGAGTTTTATAAGCATTCAAAGGATTTTATTATAACCTACAAAGCTCTTTCTTCCAACGAGAAGAATTTTTACGATGGGAAAAGCTCTTTGGAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAGAAAGGAGATGTTAGGCAGCAGACACAGCATCTCAGAGTCTGTGAAATTTTAAAAGCACGCCGTCGTGACAAATATTAACTTTGATCATGAACTTACATGAGCATTTTAAAAGGATTTGGTCCCGGGTTGCGGAGGGTAAAAGGCAATTGGGCAGAACATTACTCTGCTGCCTGCGCTCTCTCTTGTAGGCGCTGAGATGCATGCGGTGCGTGGCTTATTTTTTTTAATATCTATGCATTATGATCGTCTTTTCTTTTTTTCATACAAATTAAAACTGTATGGTGAGTCTTTTCTCTCGGTGGGGGTGTGGTGCTGAGGGCGGGGGGGGTGGGGGGGCGGCAGAGAGGGGGGGGTTTGTTGCTGGAGAGCTGAGGAATCCGCGGAGCGTTTGCTTAAGACTTTCTGTTTAAAGCTTTTTCCCCCCGCAAGGCCGGAGCAGCGCCCGGCTTTGTCCGACCGACGTGCGCTGCTTTGCTCGGCTCCTCTCCCTGCGTTCACCCGCATTTCCAGGCAGCTTTTAAAGCGCTCCATCCAGGCAACTTTGCAAGCCAGGGCTGAGCGTGGGGCTCTCTCCTTTTTTTTTGGCACAGGGGAGGGTTGTTTTGTTTCCCTCTTTGCTTTCGTGAGCTGCAGAAAGTCCCCGTTTGCAGCTCAGATGCGAAGTTCTCTTTGACTTTGATTCCCTTTTGCGTGTGTGGCGAGGACTGGAGTTAATCAGAAACTTATGCGGAACATCATATCTAGTTCCTATAATTCCGACCTCGCTCATGCTGTTTCTATACAGATAACAGATTTGCAGCCGAGCGTGCGCTCTCTTTTTTTTTTCCTCGCTTTCCCTGCACAGCTGCTCCTGCACCGCTGCCTTCAATCCCGGGCTGCTCTTTGTCAAAATAATCTCTCCGCACTCCAAATGCAGCTGCACGGGGGTCCCTTTCTGGGCTTCAAGCCCGTGCAGTGGGAAAAGCGATCGCAAAGACCCCGTGTCACCTCACCTCCGCGCTGAGATCTCCCCGTGGTTAATACCCCCCAACCCCCCACCCCCCGGCCCCCATCTATGTGGTCAGCGTGAAGGTGAGGCCGTGTGTTGCTTTTCCTCGGGATGTTGACGCTGCCTTCTGGTTCTTTTAAG
Seq C2 exon
GTGCTCCCCGAACGAGGAAGAAGAGGTGCCCCTATTCGAAATTCCAGATCAGAGAGCTGGAGAGAGAATTCTTCTTCAATGTCTATATAAACAAAGAAAAGAGGCTCCAGTTGTCTCGGATGCTGAATCTCACTGACCGACAAGTTAAAATCTGGTTTCAGAACAGAAGAATGAAAGAAAAAAAATTAAGCAGAGACCGCCTGCAGTATTTCTCTGGAAATCCCTTATTGTGAACATCTTTGTAATCCCCTCTGCTGGCGAAGTGTTTCGGGAAGGAACGGCCGCACGCGTGGCTTTGCCCTTTCAGCCGACAAAGCAACCTCAAAGTTTGAGCCTTTTCGTTACTTACATTTCTATGTCTGGGACAGTTCAGAGTAACAAAAGGAGTGAAACGTTCTTTCATTTACCAAACCGCTCAAGGACTCGAATTCCACGAACATTTTATTTAACTTCTTTTTTTTTTCCTTCTTCTTCTTCTTCTTCTTCTTTTTTTTTTTTTTTTTGGCCTGAACGAGATGGGATTCCTCCCTTCCACCCCCCCTCTCCCCTCCTCCCCCTTCTTCTTCTTCTTCTTCTTTTATTTTTTTAATTATTATTATTGTTATTATTATTCTGATGGCGATGATGATTGGCCGCCCCCGTCCCTCTGAACGCATCGCAGCGCTGTGCGGGTGTTGTTGTGACTTCACAACGCGGCCGCGTTATCCCAGGAGCGGCCAAAATCTCCCTGTAGGATCACATCCCTTCGCCTGGGGGTGAGTGTGAGTGTGTGTGTGTGTGTATGCGCGTGTGTGTGAAGCGCACCAACGCGTGTGTCCCCGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCACATCGCACCCCCCGCTCCTCTGTGTCCTTCCTCCTCCCCATGGCCAAGAGCCGGACCCTAATTTAAATCCCTGTCTGCAAGCAGAACGAAGATTCTCACCCCCCCTCCCACCCCCGCCACGCACCCTTTATATGTATATGAATACATATATGCATATATACATGCGACAGTGCCTGTGTGTATATATATACATGTATTCCGTGAGGTTCATGTTGAGTGGGAGGTGTTGGGGGGGGGGGTTTTGAAACCAAACGAAAAGACGTTTGCAATAACCGAAACGGTTTGTAAATAAATTTCGTAGTGTATTTTTTTCCCTTTTCTTTTTATTTCTTTTTTTTTTTGTCTTTTTTTTTTCTTCCTTTGTCTGAAAATGGGAGACGAAGAACGACGAGAGAACAACAGAGAAACAATCCCGAAATAATAATAATAAAAAAAGAGATGATTCTTTGTGTATGTAAAAGTGAATCCCCGGAATCCTCTGTGAAATTCTGTGGCAAATAAAGACATCGCAAGCTGTTCTACATTATGATTTTATTTGACCATTTTATTAGAATTCCCCCCTTAAAAGCCTCTTTGCGGTCATTGCGGTGCGGGTTTTTCTTCTGTCGGGGTTTTAAATACCTGCGAGCATCTCCGAAATATCATCATCCATATTCATGGCGCTGCAATCTGCTCCGAGAGGAGCGGGCTTTGAGGAGACCTCCGCCTCTGAGCCCACGTTTGGCTGCGAAGCGTTCGGCACCGAACCGCGATGGATGGGCTTTTCTCTCGGCCCTCAATTCGGCTCCCGATGCCTGCCTTTATTTTCCGGCCTCAGTTCATCTTTCTTTCTTTCTTTCTTTCTTTTTTTCCTTTTATTTTTTGCCACAACAACCCCTCACGTTCTCTTTTTTGTTCGTTCCTTTTAATGAAACGAATGGCACCACGGAGCTGCGTTTCCGAAAGGACACCGCACCTTCTCCCTGCAGAGCGCAAATGCAAAGTCAAGTCCTTCGATTCCCGCTTAAGAAAACAAGTTCAATCCCATGCACGGGGGCATCACCGTCATTTTTTCTCCCCCCCTCTGTTCTCACAATGACTTTTCTTTTCTGTCTCGCAGCCGCACAACGTTTTCGAGGACAAAGAAGACGCGGCGCACGAGTTTGGGGTCAATGCTGCGGTTGGGAGTGTTGGTTTGGAGGGTTTGGGGGGGTCCGGGTCGATCTGAACGCTCTCCTCTCGATGTGGAGCGATGGGATCGTGCATATGGACGGGGTGGGGGTGGGGGGGAGGGGGTTTGAGAAGAAAAATAGAAGAGGGGATGAAAAAAAAAAGCCCAAAACCGGCAGCAAAGAAACAACGCATCGTATTCCCATCCATTGAGCGTGTTCCTGTAAAATTCTCATCCTCGCTTTTAAATACAGCCCTTGTGGAATGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000026100:ENSGALT00000044866:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.442 A=NA C2=0.182
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=63.4)
A:
NA
C2:
PF0004624=Homeobox=WD(100=73.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAAAACGAGAGCGCGTACA
R:
GCACCTCTTCTTCCTCGTTCG
Band lengths:
356-1689
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]